Biomass chitosan-derived porous carbon-based materials take the advantage of light weight, adjustable intrinsic conductivity, and environmental friendliness, attracting more attention in the field of electromagnetic compatibility. However, exploring a facile fabrication method to achieve rational structure design and electrical-magnetic coupling for electromagnetic absorption performance enhancement still remains challenging. Here, a unique honeycomb-like porous cobalt/carbon aerogel is fabricated through the directional freezing-drying and carbonization process, and abundant and even-distributed cobalt particles in-situ grow on the carbon skeletons. The aerogel exhibits an impressive electromagnetic wave absorption performance of a −75.8-dB absorption intensity and a −256.9-dB mm−1 specific reflection loss at a low filling content (10%), as well as an 8.53-GHz effective absorption bandwidth. Besides, the aerogel also demonstrates classy radar stealth and thermal insulation performance. The eco-friendly, easily fabricated, and high-performance cobalt/carbon aerogel suggests broad application prospects for electromagnetic compatibility and protection, thermal management, and multifarious electron devices.